ZSwcPath ZNeuronTracer::trace(double x, double y, double z)
{
if (m_traceWorkspace->trace_mask == NULL) {
m_traceWorkspace->trace_mask =
C_Stack::make(GREY, C_Stack::width(m_stack), C_Stack::height(m_stack),
C_Stack::depth(m_stack));
Zero_Stack(m_traceWorkspace->trace_mask);
}
double pos[3];
pos[0] = x;
pos[1] = y;
pos[2] = z;
Local_Neuroseg *locseg = New_Local_Neuroseg();
Set_Neuroseg(&(locseg->seg), 3.0, 0.0, 11.0, TZ_PI_4, 0.0, 0.0, 0.0, 1.0);
Set_Neuroseg_Position(locseg, pos, NEUROSEG_CENTER);
Locseg_Fit_Workspace *ws =
(Locseg_Fit_Workspace*) m_traceWorkspace->fit_workspace;
Local_Neuroseg_Optimize_W(locseg, m_stack, 1.0, 1, ws);
Trace_Record *tr = New_Trace_Record();
tr->mask = ZERO_BIT_MASK;
Trace_Record_Set_Fix_Point(tr, 0.0);
Trace_Record_Set_Direction(tr, DL_BOTHDIR);
Locseg_Node *p = Make_Locseg_Node(locseg, tr);
Locseg_Chain *locseg_chain = Make_Locseg_Chain(p);
Trace_Workspace_Set_Trace_Status(m_traceWorkspace, TRACE_NORMAL,
TRACE_NORMAL);
Trace_Locseg(m_stack, 1.0, locseg_chain, m_traceWorkspace);
Locseg_Chain_Remove_Overlap_Ends(locseg_chain);
Locseg_Chain_Remove_Turn_Ends(locseg_chain, 1.0);
int n;
Geo3d_Circle *circles =
Locseg_Chain_To_Geo3d_Circle_Array(locseg_chain, NULL, &n);
ZSwcPath path;
for (int i = 0; i < n; ++i) {
Swc_Tree_Node *tn = SwcTreeNode::makePointer(circles[i].center[0],
circles[i].center[1], circles[i].center[2], circles[i].radius);
if (!path.empty()) {
SwcTreeNode::setParent(tn, path.back());
}
path.push_back(tn);
}
return path;
}
ZSwcPath ZNeuronTracer::trace(double x, double y, double z)
{
setTraceScoreThreshold(TRACING_INTERACTIVE);
if (m_traceWorkspace->trace_mask == NULL) {
m_traceWorkspace->trace_mask =
C_Stack::make(GREY, getStack()->width(), getStack()->height(),
getStack()->depth());
Zero_Stack(m_traceWorkspace->trace_mask);
}
Stack *stackData = getIntensityData();
ZIntPoint stackOffset = getStack()->getOffset();
double pos[3];
pos[0] = x - stackOffset.getX();
pos[1] = y - stackOffset.getY();
pos[2] = z - stackOffset.getZ();
/* alloc <locseg> */
Local_Neuroseg *locseg = New_Local_Neuroseg();
Set_Neuroseg(&(locseg->seg), 3.0, 0.0, 11.0, TZ_PI_4, 0.0, 0.0, 0.0, 1.0);
Set_Neuroseg_Position(locseg, pos, NEUROSEG_CENTER);
Locseg_Fit_Workspace *ws =
(Locseg_Fit_Workspace*) m_traceWorkspace->fit_workspace;
Local_Neuroseg_Optimize_W(locseg, stackData, 1.0, 1, ws);
Trace_Record *tr = New_Trace_Record();
tr->mask = ZERO_BIT_MASK;
Trace_Record_Set_Fix_Point(tr, 0.0);
Trace_Record_Set_Direction(tr, DL_BOTHDIR);
/* consume <locseg> */
Locseg_Node *p = Make_Locseg_Node(locseg, tr);
/* alloc <locseg_chain> */
Locseg_Chain *locseg_chain = Make_Locseg_Chain(p);
Trace_Workspace_Set_Trace_Status(m_traceWorkspace, TRACE_NORMAL,
TRACE_NORMAL);
Trace_Locseg(stackData, 1.0, locseg_chain, m_traceWorkspace);
Locseg_Chain_Remove_Overlap_Ends(locseg_chain);
Locseg_Chain_Remove_Turn_Ends(locseg_chain, 1.0);
int n;
/* alloc <circles> */
Geo3d_Circle *circles =
Locseg_Chain_To_Geo3d_Circle_Array(locseg_chain, NULL, &n);
/* free <locseg_chain> */
Kill_Locseg_Chain(locseg_chain);
ZSwcPath path;
if (n > 0) {
// bool hit = false;
int start = 0;
int end = n;
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[0].center) > 0) {
for (int i = 1; i < n; ++i) {
start = i - 1;
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[i].center) == 0) {
break;
}
}
}
if (n > 1) {
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[n - 1].center) > 0) {
for (int i = n - 2; i >= 0; --i) {
end = i + 2;
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[i].center) == 0) {
break;
}
}
}
}
for (int i = start; i < end; ++i) {
Swc_Tree_Node *tn = SwcTreeNode::makePointer(circles[i].center[0],
circles[i].center[1], circles[i].center[2], circles[i].radius);
if (!path.empty()) {
SwcTreeNode::setParent(tn, path.back());
}
SwcTreeNode::translate(tn, stackOffset);
path.push_back(tn);
}
}
/* free <circles> */
if (circles != NULL) {
free(circles);
}
return path;
}